X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=803f323d480811fd8f53bea6cf75af3e5de1b38e;hb=feaa53e0e6dea15a236b99097347df52c21db896;hp=b6d43ea2e8e9f9100b99cf2c22c9e7f6621b8516;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index b6d43ea..803f323 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,18 +1,40 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ + package jalview.appletgui; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.schemes.*; +import java.util.*; + import java.awt.*; import java.awt.event.*; -public class APopupMenu extends java.awt.PopupMenu +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.schemes.*; +import jalview.io.AppletFormatAdapter; + +public class APopupMenu + extends java.awt.PopupMenu implements ActionListener, ItemListener { Menu groupMenu = new Menu(); - Menu analyze = new Menu(); - Menu defineMenu = new Menu(); - Menu groupName = new Menu(); - Menu groupAnnotation = new Menu(); + MenuItem editGroupName = new MenuItem(); protected MenuItem clustalColour = new MenuItem(); protected MenuItem zappoColour = new MenuItem(); protected MenuItem taylorColour = new MenuItem(); @@ -28,19 +50,33 @@ public class APopupMenu extends java.awt.PopupMenu MenuItem noColourmenuItem = new MenuItem(); protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - - AlignmentPanel ap; - Menu sequenceMenu = new Menu(); - MenuItem sequenceName = new MenuItem(); - Menu residueMenu = new Menu(); - MenuItem annotateResidue = new MenuItem(); - - Sequence sequence; + final AlignmentPanel ap; MenuItem unGroupMenuItem = new MenuItem(); - MenuItem outline = new MenuItem(); MenuItem nucleotideMenuItem = new MenuItem(); - - public APopupMenu(AlignmentPanel ap, Sequence seq) + Menu colourMenu = new Menu(); + CheckboxMenuItem showBoxes = new CheckboxMenuItem(); + CheckboxMenuItem showText = new CheckboxMenuItem(); + CheckboxMenuItem showColourText = new CheckboxMenuItem(); + Menu editMenu = new Menu("Edit"); + MenuItem copy = new MenuItem("Copy (Jalview Only)"); + MenuItem cut = new MenuItem("Cut (Jalview Only)"); + MenuItem toUpper = new MenuItem("To Upper Case"); + MenuItem toLower = new MenuItem("To Lower Case"); + MenuItem toggleCase = new MenuItem("Toggle Case"); + Menu outputmenu = new Menu(); + Menu seqMenu = new Menu(); + MenuItem pdb = new MenuItem(); + MenuItem hideSeqs = new MenuItem(); + MenuItem repGroup = new MenuItem(); + MenuItem sequenceName = new MenuItem("Edit Name/Description"); + MenuItem sequenceFeature = new MenuItem("Create Sequence Feature"); + MenuItem editSequence = new MenuItem("Edit Sequence"); + + Sequence seq; + MenuItem revealAll = new MenuItem(); + Menu menu1 = new Menu(); + + public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { /////////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -49,482 +85,805 @@ public class APopupMenu extends java.awt.PopupMenu // If from the IDPanel, we must display the sequence menu ////////////////////////////////////////////////////////// - this.ap = ap; - sequence = seq; + this.ap = apanel; + this.seq = seq; try - { jbInit(); } - catch(Exception e) - { e.printStackTrace(); } + { + jbInit(); + } + catch (Exception e) + { + e.printStackTrace(); + } + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; + i++) + { + MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter. + WRITEABLE_FORMATS[i]); - if(seq!=null) - residueMenu.setEnabled(false); - else - sequenceMenu.setEnabled(false); + item.addActionListener(this); + outputmenu.add(item); + } - } - private void jbInit() throws Exception - { - groupMenu.setLabel("Group"); - analyze.setLabel("Analyze"); - analyze.addActionListener(new java.awt.event.ActionListener() + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null && sg.getSize() > 0) { - public void actionPerformed(ActionEvent e) + editGroupName.setLabel(sg.getName()); + showText.setState(sg.getDisplayText()); + showColourText.setState(sg.getColourText()); + showBoxes.setState(sg.getDisplayBoxes()); + if (!ap.av.alignment.getGroups().contains(sg)) { - analyze_actionPerformed(e); + groupMenu.remove(unGroupMenuItem); } - }); - defineMenu.setLabel("Define"); - groupName.setLabel("Name"); - groupName.addActionListener(new java.awt.event.ActionListener() + + } + else { - public void actionPerformed(ActionEvent e) - { - groupName_actionPerformed(e); - } - }); - groupAnnotation.setEnabled(false); - groupAnnotation.setLabel("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() + remove(hideSeqs); + remove(groupMenu); + } + + if (links != null) { - public void actionPerformed(ActionEvent e) + Menu linkMenu = new Menu("Link"); + MenuItem item; + String link; + for (int i = 0; i < links.size(); i++) { - groupAnnotation_actionPerformed(e); + link = links.elementAt(i).toString(); + final String target = link.substring(0, link.indexOf("|")); + item = new MenuItem(target); + + final String url; + + if (link.indexOf("$SEQUENCE_ID$") > -1) + { + String id = seq.getName(); + if (id.indexOf("|") > -1) + { + id = id.substring(id.lastIndexOf("|") + 1); + } + + url = link.substring(link.indexOf("|") + 1, + link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + } + else + { + url = link.substring(link.lastIndexOf("|") + 1); + } + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.alignFrame.showURL(url, target); + } + }); + linkMenu.add(item); } - }); - sequenceMenu.setLabel("Sequence"); - sequenceName.setLabel("Edit name"); - sequenceName.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) + if (seq != null) { - sequenceName_actionPerformed(e); + seqMenu.add(linkMenu); } - }); - residueMenu.setLabel("Residue"); - annotateResidue.setEnabled(false); - annotateResidue.setActionCommand("annotate residue"); - annotateResidue.setLabel("annotate residue???"); - unGroupMenuItem.setLabel("Remove Group"); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) + else { - unGroupMenuItem_actionPerformed(e); + add(linkMenu); } - }); + } + if (seq != null) + { + seqMenu.setLabel(seq.getName()); + repGroup.setLabel("Represent Group with " + seq.getName()); + } + else + { + remove(seqMenu); + } - outline.setLabel("Border colour"); - outline.addActionListener(new java.awt.event.ActionListener() + if (!ap.av.hasHiddenRows) { - public void actionPerformed(ActionEvent e) - { - outline_actionPerformed(e); - } - }); - nucleotideMenuItem.setLabel("Nucleotide"); - nucleotideMenuItem.addActionListener(new ActionListener() + remove(revealAll); + } + } + + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == abovePIDColour) { - public void actionPerformed(ActionEvent e) - { - nucleotideMenuItem_actionPerformed(e); - } - }); + abovePIDColour_itemStateChanged(); + } + else if (evt.getSource() == showColourText) + { + showColourText_itemStateChanged(); + } + else if (evt.getSource() == showText) + { + showText_itemStateChanged(); + } + else if (evt.getSource() == showBoxes) + { + showBoxes_itemStateChanged(); + } + } - add(groupMenu); - this.add(sequenceMenu); - this.add(residueMenu); - groupMenu.add(defineMenu); - groupMenu.add(unGroupMenuItem); - groupMenu.addSeparator(); - groupMenu.add(analyze); - defineMenu.add(groupName); - defineMenu.add(groupAnnotation); - defineMenu.addSeparator(); - defineMenu.add(outline); - defineMenu.addSeparator(); - defineMenu.add(noColourmenuItem); - defineMenu.add(clustalColour); - defineMenu.add(BLOSUM62Colour); - defineMenu.add(PIDColour); - - defineMenu.add(zappoColour); - defineMenu.add(taylorColour); - defineMenu.add(hydrophobicityColour); - defineMenu.add(helixColour); - defineMenu.add(strandColour); - defineMenu.add(turnColour); - defineMenu.add(buriedColour); - defineMenu.add(nucleotideMenuItem); - - defineMenu.add(userDefinedColour); - - defineMenu.addSeparator(); - defineMenu.add(abovePIDColour); - defineMenu.add(conservationMenuItem); - - sequenceMenu.add(sequenceName); - residueMenu.add(annotateResidue); + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + if (source == clustalColour) + { + clustalColour_actionPerformed(); + } + else if (source == zappoColour) + { + zappoColour_actionPerformed(); + } + else if (source == taylorColour) + { + taylorColour_actionPerformed(); + } + else if (source == hydrophobicityColour) + { + hydrophobicityColour_actionPerformed(); + } + else if (source == helixColour) + { + helixColour_actionPerformed(); + } + else if (source == strandColour) + { + strandColour_actionPerformed(); + } + else if (source == turnColour) + { + turnColour_actionPerformed(); + } + else if (source == buriedColour) + { + buriedColour_actionPerformed(); + } + else if (source == nucleotideMenuItem) + { + nucleotideMenuItem_actionPerformed(); + } - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + else if (source == userDefinedColour) { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); + userDefinedColour_actionPerformed(); + } + else if (source == PIDColour) + { + PIDColour_actionPerformed(); + } + else if (source == BLOSUM62Colour) + { + BLOSUM62Colour_actionPerformed(); + } + else if (source == noColourmenuItem) + { + noColourmenuItem_actionPerformed(); + } + else if (source == conservationMenuItem) + { + conservationMenuItem_itemStateChanged(); + } + else if (source == unGroupMenuItem) + { + unGroupMenuItem_actionPerformed(); + } - clustalColour.setLabel("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() + else if (source == sequenceName) { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(new java.awt.event.ActionListener() + editName(); + } + else if (source == pdb) { - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(new java.awt.event.ActionListener() + addPDB(); + } + else if (source == hideSeqs) { - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() + hideSequences(false); + } + else if (source == repGroup) { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); - helixColour.setLabel("Helix propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() + hideSequences(true); + } + else if (source == revealAll) { - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(e); - } - }); - strandColour.setLabel("Strand propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() + ap.av.showAllHiddenSeqs(); + } + + else if (source == editGroupName) { - public void actionPerformed(ActionEvent e) + EditNameDialog dialog = new EditNameDialog( + getGroup().getName(), + getGroup().getDescription(), + " Group Name", + "Group Description", + ap.alignFrame, + "Edit Group Name / Description", + 500,100, true); + + if (dialog.accept) { - strandColour_actionPerformed(e); + getGroup().setName(dialog.getName().replace(' ', '_')); + getGroup().setDescription(dialog.getDescription()); } - }); - turnColour.setLabel("Turn propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() + + } + else if (source == copy) { - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(e); - } - }); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() + ap.alignFrame.copy_actionPerformed(); + } + else if (source == cut) { - public void actionPerformed(ActionEvent e) + ap.alignFrame.cut_actionPerformed(); + } + else if(source == editSequence) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + + if(sg!=null) { - buriedColour_actionPerformed(e); + if (seq == null) + seq = (Sequence) sg.getSequenceAt(0); + + EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString( + sg.getStartRes(), + sg.getEndRes() + 1), + null, + "Edit Sequence ", + null, + + ap.alignFrame, + "Edit Sequence", + 500, 100, true); + + if (dialog.accept) + { + EditCommand editCommand = new EditCommand( + "Edit Sequences", EditCommand.REPLACE, + dialog.getName().replace(' ', ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes()+1, ap.av.alignment + ); + + ap.alignFrame.addHistoryItem(editCommand); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } } - }); - abovePIDColour.setLabel("Above % Identity"); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() + } + else if (source == toUpper || source == toLower || source == toggleCase) { - public void actionPerformed(ActionEvent e) + SequenceGroup sg = ap.av.getSelectionGroup(); + Vector regions = new Vector(); + if (sg != null) { - abovePIDColour_actionPerformed(e); + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do + { + if (ap.av.hasHiddenColumns) + { + if (start == 0) + { + start = ap.av.colSel.adjustForHiddenColumns(start); + } + + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + { + end = sg.getEndRes() + 1; + } + if (end > sg.getEndRes()) + { + end = sg.getEndRes() + 1; + } + } + + regions.addElement(new int[] + {start, end}); + + if (ap.av.hasHiddenColumns) + { + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + } + while (end < sg.getEndRes()); + + int[][] startEnd = new int[regions.size()][2]; + for (int i = 0; i < regions.size(); i++) + { + startEnd[i] = (int[]) regions.elementAt(i); + } + + String description; + int caseChange; + + if (source == toggleCase) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if (source == toUpper) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), + startEnd, caseChange + ); + + ap.alignFrame.addHistoryItem(caseCommand); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } - }); - userDefinedColour.setLabel("User Defined"); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + } + else if(source == sequenceFeature) { - public void actionPerformed(ActionEvent e) + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) { - userDefinedColour_actionPerformed(e); + return; } - }); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) + + int gSize = sg.getSize(); + SequenceI[] seqs = new SequenceI[gSize]; + SequenceFeature[] features = new SequenceFeature[gSize]; + + for (int i = 0; i < gSize; i++) { - PIDColour_actionPerformed(e); + seqs[i] = sg.getSequenceAt(i); + int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); + int end = sg.findEndRes(sg.getSequenceAt(i)); + features[i] = new SequenceFeature(null, null, null, start, end, + "Jalview"); } - }); - BLOSUM62Colour.setLabel("BLOSUM62"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) + + if (ap.seqPanel.seqCanvas.getFeatureRenderer() + .amendFeatures(seqs, features, true, ap)) { - BLOSUM62Colour_actionPerformed(e); + ap.alignFrame.sequenceFeatures.setState(true); + ap.av.showSequenceFeatures(true); + ap.highlightSearchResults(null); } - }); - conservationMenuItem.setLabel("Conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(e); - } - }); + } + else + { + outputText(evt); + } + + } + + void outputText(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Selection output - " + e.getActionCommand(), + 600, 500); + cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( + e.getActionCommand(), + new Alignment(ap.av.getSelectionAsNewSequence()), + ap.av.showJVSuffix)); } - void refresh() + void editName() { - SequenceGroup sg = getGroup(); - SuperGroup superG = ap.av.alignment.getSuperGroup( sg ); - if( superG !=null) - superG.setSuperGroupProperties( sg ); + EditNameDialog dialog = new EditNameDialog( + seq.getName(), + seq.getDescription(), + " Sequence Name", + "Sequence Description", + ap.alignFrame, + "Edit Sequence Name / Description", + 500,100, true); + + if (dialog.accept) + { + seq.setName(dialog.getName()); + seq.setDescription(dialog.getDescription()); + ap.paintAlignment(false); + } + } + + void addPDB() + { + if(seq.getPDBId()!=null) + { + PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement(); + + if ( ap.av.applet.jmolAvailable ) + new jalview.appletgui.AppletJmol(entry, + new Sequence[]{seq}, + null, + ap, + AppletFormatAdapter.URL); + else + new MCview.AppletPDBViewer(entry, + new Sequence[]{seq}, + null, + ap, + AppletFormatAdapter.URL); + + } + else + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + cap.setText("Paste your PDB file here."); + cap.setPDBImport(seq); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300); + } + } + + private void jbInit() + throws Exception + { + groupMenu.setLabel("Group"); + groupMenu.setLabel("Selection"); + sequenceFeature.addActionListener(this); + + editGroupName.addActionListener(this); + unGroupMenuItem.setLabel("Remove Group"); + unGroupMenuItem.addActionListener(this); + + nucleotideMenuItem.setLabel("Nucleotide"); + nucleotideMenuItem.addActionListener(this); + conservationMenuItem.addItemListener(this); + abovePIDColour.addItemListener(this); + colourMenu.setLabel("Group Colour"); + showBoxes.setLabel("Boxes"); + showBoxes.setState(true); + showBoxes.addItemListener(this); + sequenceName.addActionListener(this); + + showText.setLabel("Text"); + showText.addItemListener(this); + showColourText.setLabel("Colour Text"); + showColourText.addItemListener(this); + outputmenu.setLabel("Output to Textbox..."); + seqMenu.setLabel("Sequence"); + pdb.setLabel("View PDB Structure"); + hideSeqs.setLabel("Hide Sequences"); + repGroup.setLabel("Represent Group with"); + revealAll.setLabel("Reveal All"); + menu1.setLabel("Group"); + add(groupMenu); + this.add(seqMenu); + this.add(hideSeqs); + this.add(revealAll); + groupMenu.add(editGroupName); + groupMenu.add(editMenu); + groupMenu.add(outputmenu); + groupMenu.add(sequenceFeature); + groupMenu.add(menu1); + + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideMenuItem); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + + clustalColour.setLabel("Clustalx colours"); + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + abovePIDColour.setLabel("Above % Identity"); + + userDefinedColour.setLabel("User Defined"); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62"); + BLOSUM62Colour.addActionListener(this); + conservationMenuItem.setLabel("Conservation"); + + editMenu.add(copy); + copy.addActionListener(this); + editMenu.add(cut); + cut.addActionListener(this); + + editMenu.add(editSequence); + editSequence.addActionListener(this); + + editMenu.add(toUpper); + toUpper.addActionListener(this); + editMenu.add(toLower); + toLower.addActionListener(this); + editMenu.add(toggleCase); + seqMenu.add(sequenceName); + seqMenu.add(pdb); + seqMenu.add(repGroup); + menu1.add(unGroupMenuItem); + menu1.add(colourMenu); + menu1.add(showBoxes); + menu1.add(showText); + menu1.add(showColourText); + toggleCase.addActionListener(this); + pdb.addActionListener(this); + hideSeqs.addActionListener(this); + repGroup.addActionListener(this); + revealAll.addActionListener(this); + } - ap.seqPanel.repaint(); + void refresh() + { + ap.paintAlignment(true); } - protected void clustalColour_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); refresh(); } - protected void zappoColour_actionPerformed(ActionEvent e) + protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); } - protected void taylorColour_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); } - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); } - protected void helixColour_actionPerformed(ActionEvent e) + protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); } - protected void strandColour_actionPerformed(ActionEvent e) + protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); } - protected void turnColour_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); } - protected void buriedColour_actionPerformed(ActionEvent e) + protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); } - public void nucleotideMenuItem_actionPerformed(ActionEvent e) + public void nucleotideMenuItem_actionPerformed() { getGroup().cs = new NucleotideColourScheme(); refresh(); } - - - protected void abovePIDColour_actionPerformed(ActionEvent e) + protected void abovePIDColour_itemStateChanged() { SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. + hiddenRepSequences), 0, ap.av.alignment.getWidth())); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); - if (sg.cs instanceof ResidueColourScheme) - ( (ResidueColourScheme)sg. cs).setThreshold(threshold); - else if (sg.cs instanceof ScoreColourScheme) - ( (ScoreColourScheme) sg.cs).setThreshold(threshold); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); - SliderPanel.showPIDSlider(); + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + SliderPanel.showPIDSlider(); } else // remove PIDColouring { - ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; - rcs.setThreshold(0); - sg.cs = rcs; + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); } refresh(); } - - protected void userDefinedColour_actionPerformed(ActionEvent e) + protected void userDefinedColour_actionPerformed() { - UserDefinedColours chooser = new UserDefinedColours( ap, getGroup()); + new UserDefinedColours(ap, getGroup()); } - protected void PIDColour_actionPerformed(ActionEvent e) + protected void PIDColour_actionPerformed() { - + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. + hiddenRepSequences), 0, + ap.av.alignment.getWidth())); + refresh(); } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void BLOSUM62Colour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. + hiddenRepSequences), 0, + ap.av.alignment.getWidth())); refresh(); } - - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_itemStateChanged() { SequenceGroup sg = getGroup(); - - if(conservationMenuItem.getState()) + if (sg.cs == null) { + return; + } - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.sequences, 0, - ap.av.alignment.getWidth()); + if (conservationMenuItem.getState()) + { - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(ap.av. + hiddenRepSequences), 0, + ap.av.alignment.getWidth()); + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); - sg.cs = ccs; + sg.cs.setConservation(c); - SliderPanel.setConservationSlider(ap, ccs, sg.getName()); + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - sg.cs = ccs.cs; + sg.cs.setConservation(null); } - refresh(); + refresh(); } - protected void groupAnnotation_actionPerformed(ActionEvent e) + SequenceGroup getGroup() { + SequenceGroup sg = ap.av.getSelectionGroup(); + + // this method won't add a new group if it already exists + if (sg != null) + { + ap.av.alignment.addGroup(sg); + } + return sg; } - protected void groupName_actionPerformed(ActionEvent e) + void unGroupMenuItem_actionPerformed() { - /* SequenceGroup sg = getGroup(); - String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE); - if(reply==null) - return; - - sg.setName(reply); - groupName.setLabel(reply);*/ + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + ap.paintAlignment(true); } + public void showColourText_itemStateChanged() + { + getGroup().setColourText(showColourText.getState()); + refresh(); + } - protected void analyze_actionPerformed(ActionEvent e) + public void showText_itemStateChanged() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300); - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for(int i=0; i